Matt, when I converted some of my LOR S3 sequences from last year, I got error messages from most or all channels assigned to Universe 2 and 3. My sequences have no LOR networks defined at all. That was with "Single" LOR Sequence Mapping checked.
When I changed to Multi and converted the same sequences, I did not get those errors and they appear to have converted perfectly. I've been waiting for this feature because the older 2012b wouldn't give me a good Conductor file.
Is the behavior between Single and Multi mapping as you expected? Could you better explain the difference between them?